fixed flipped modules

bayespairing/src/BayesPairing.py

@@ -480,7 +480,7 @@ def parse_sequence(seq, modules, ss, dataset, BNs, t=-10, samplesize=20000, Lamb
             #print(seq)
             #print(struct)
             if not str(r.node.positions) in modules_predicted[r.module.ID]:
-                #print("about to score",r.seq, r.rotation, r.pos)
+                #print("about to score",r.seq, r.rotation, r.pos, r.module.nodes)
                 r.eval(fold_compound=fc)
                 #print("SCORED MODULE",r.module.ID, r.seq, r.pos, r.score)
                 #print("PASSING THRESHOLD",r.score,t)

bayespairing/src/scanning/src/classes/ScanResult.py

@@ -55,8 +55,8 @@ class ExactScanResult:
         #print("FOUND SEQUENCE:",self.seq)
 
         #print("UNROTATED GAPS",self.module.gaps_per_strand)
-        if rotation:
-            self.rotate(rotation)
+        #if rotation:
+        #    self.rotate(rotation)
         #print("LEN POS",self.pos,"LEN SEQ",self.seq, "ROTATION",rotation)
         #print("DONE ROTATION, CURRENT SEQUENCE", self.seq)
 
@@ -100,8 +100,9 @@ class ExactScanResult:
     def reintegrate_module_gaps_to_sse_sequence_and_positions(self):
         #print("REGAPPING MODULE", self.module.ss, self.module.stackings, self.gaps,self.seq,self.pos)
 
-        positions = self.pos
-        gaps = self.rotate_list(self.gaps)
+        positions = self.rotate_list(self.pos)
+        #gaps = self.rotate_list(self.gaps) this does not help, the gaps shouldnt rotate on the module
+        gaps = self.gaps
         seq = self.seq
 
         new_seq = ""
@@ -113,8 +114,8 @@ class ExactScanResult:
                     if ind not in gaps[0]:
                         new_seq += nuc
         else:
-            #for strand,subseq in enumerate(self.rotate_list(seq.split("&"))):
-            for strand,subseq in enumerate(seq.split("&")):
+            for strand,subseq in enumerate(self.rotate_list(seq.split("&"))):
+            #for strand,subseq in enumerate(seq.split("&")):
                 #print("STRAND",strand,"GAPS",gaps, seq, seq.split("&"))
                 if not gaps[strand]:
                     new_seq+=subseq
@@ -138,7 +139,7 @@ class ExactScanResult:
                         new_strand.append(pos)
                 new_pos.append(new_strand)
         self.module_positions = new_pos
-        #print("POST REGAPPED SEQUENCE:",new_pos,new_seq)
+        #print("POST REGAPPED SEQUENCE:",new_pos,new_seq, gaps)
         #still on tryout.. does it affect anything else to name pos here immediately?
         self.pos = new_pos